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kevinkovalchik / RawTools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Apache License 2.0
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More consistent column/row names #35

Closed sorenwacker closed 5 years ago

sorenwacker commented 5 years ago

Hi,

I noticed that the column/row names have different formats and even different names for the same content in the files generated by RawTools. For example, the metrics file contains the field RawFile that contains the path of the raw file, while in the QcDataTable the column name is called FileName. Some other examples:

The QcDataTable: Ms1ScanRate(/s) MedianMs3FillTime(ms)

The Metrics file: TotalAnalysisTime(min): MS1ScanRate(/sec):
MedianPeakWidthAt10Percent(s):

My suggestion is to use the same format for the units, preferably something like [1/s] with square brackets and SI-units, in all files and use the same identifier for the same contents.

kevinkovalchik commented 5 years ago

Hi Soren,

Thanks for bringing this up. I'm working on some other updates that I plan to release in the the next month or two. I'll be sure to address this as well, unless it would help you to have it done sooner. Is this something that is impeding your workflows right now, or does it just bother your good sense? :)

Kevin

sorenwacker commented 5 years ago

Just a sense of consistency. I can rename the fields.

kevinkovalchik commented 5 years ago

Hi @soerendip,

v2.0.0 just got released. I made an effort to align all the metric names between the different data files. Let me know if you see anything else to fix.

Also, as we talked about quite a while ago, the "parse" and "qc" functions are no longer separate. You can mix whatever parts of the parse functionality you want in with qc.